Chapter 3: The Cellular Level of Organization

The Cellular Level of Organization

• The primary responsibility of each cell is to contribute to homeostasis.

• Homeostasis is a dynamic state of balance within parameters compatible with life.

• The concept of a cell started with Robert Hooke's microscopic observations of dead cork tissue in 1665.

• Hooke coined the term “cell” based on the resemblance of the small subdivisions in the cork tissue to monks' rooms, called cells.

• About 10 years later, Antonie van Leeuwenhoek was the first person to observe living and moving cells under a microscope.

• In the following century, the theory that cells represented the basic unit of life would develop.

• German scientists Theodor Schwann, Matthias Schleiden, and Rudolph Virchow are given credit for the formulation of the Cell Theory.

Cell Theory: 4 Concepts

1. A cell is the structural and functional unit of life.

2. An organism’s functions depend on the functions of individual cells and collective cell functions.

3. Biochemical activities of cells are dictated by their shapes or forms and the number of specific subcellular structures.

4. Continuity of life has a cellular basis.

• Over 200 different types of human cells.

• Cells differ in size, shape, subcellular components, and functions.

The Generalized Cell

• All cells have some common structures and functions.

• A prototypical human cell has 3 basic parts:

  1. Plasma membrane: a flexible outer boundary.

  2. Cytoplasm: everything between the membrane and the nucleus.

     • cytosol = intracellular fluid

     • organelles = subcellular structures with specific functions; compartmentalization of chemical reactions

  3. Nucleus: the control center of the cell; DNA.

The Cell Membrane (Plasma Membrane)

• It's a pliable but sturdy barrier that surrounds the cytoplasm of the cell.

• Composed primarily of back-to-back phospholipids (a “bilayer”) of 3 types of lipid molecules.

  1. Cholesterol

  2. Glycolipids are scattered among a double row (“bilayer”) of

  3. Phospholipid molecules.

• Each phospholipid molecule is amphipathic (it has both a polar & nonpolar region).

• The polar parts (heads) are hydrophilic and face a watery environment on both surfaces.

• The nonpolar parts (tails) are hydrophobic and line up next to each other in the interior.

• This combination adds to the fluidity of the tails that are constantly in motion.

• Some lipid tails consist of saturated fatty acids & some contain unsaturated fatty acids.

• Because the phosphate groups are polar and hydrophilic, they are attracted to water in the intracellular fluid (ICF).

• ICF is the fluid interior of the cell.

• The phosphate groups are also attracted to the extracellular fluid (ECF).

• ECF is the fluid environment outside the enclosure of the cell membrane.

• Interstitial fluid (IF) is the term given to extracellular fluid not contained within blood vessels.

• Because the lipids tails are hydrophobic, they meet in the inner region of the membrane,

• Thereby, excluding the watery ICF and ECF from this space.

• An important feature of the membrane is that it remains fluid; the lipids and proteins in it are not rigidly locked in place à Fluid-Mosaic Model.

Six Functions of the Cell Membrane Proteins

1. Transport

2. Receptors for signal transduction

3. Attachment to the cytoskeleton and extracellular matrix

4. Enzymatic activity

5. Intercellular joining

6. Cell-cell recognition

Membrane Proteins

• The bilayer forms the basis of the cell membrane (CM), but it is peppered throughout with various proteins.

  1. Integral proteins; usually transmembrane

     • Embedded in the CM, examples are:

       • Channel/transporter proteins; selectively allows particular materials, such as ions, to pass into or out of the cell.

       • Receptor proteins; a type of recognition protein that can selectively bind a specific molecule à ligand

       • Glycoprotein; a protein with carbohydrate molecules attached which extend into the extracellular matrix.

         • Aid in cell recognition

         • Glycocalyx; is a fuzzy-appearing coating around the cell formed from glycoproteins, glycolipids, and other carbohydrates.

           • Has various roles:

             • cell-to-cell binding,

             • may contain receptors for hormones,

             • it may have enzymes to break down nutrients,

             • cell “identity.”

  2. Peripheral proteins

     • Are typically found on the inner or outer surface of the lipid bilayer

     • But can also be loosely attached to the internal or external surface of an integral protein.

     • Typically perform a specific function for the cell.

       • On the surface of intestinal cells and act as digestive enzymes

       • Includes filaments on the intracellular surface for membrane support and stability.

       • Function as enzymes; motor proteins for shape change during cell division and muscle contraction; cell-to-cell connections

Transport Across the Cell Membrane (CM)

• The cell membrane can regulate the concentration of substances inside the cell.

• These substances include ions such as Ca^{2+}, Na^+, K^+, and Cl^-; nutrients including sugars, fatty acids, and amino acids; and waste products, particularly carbon dioxide (CO_2), which must leave the cell.

• The membrane’s lipid bilayer structure provides the first level of control.

• The phospholipids are tightly packed together, and the membrane has a hydrophobic interior.

• This structure causes the membrane to be selectively permeable.

• A membrane that has selective permeability allows only substances meeting certain criteria to pass through it unaided.

• Only relatively small, nonpolar materials can move through the lipid bilayer of the CM and other lipids, O2 & CO2 gases, and alcohol.

• Water-soluble materials, like glucose, amino acids, and electrolytes, need assistance to cross the CM because they are repelled by the hydrophobic tails of the phospholipid bilayer.

• All substances that move through the CM do so by one of 2 general methods, which are categorized based on whether or not energy (ATP) is required.

Passive Transport

• The movement of substances across the CM without the expenditure of cellular energy.

Active Transport

• The movement of substances across the CM using ATP.

• The membrane can maintain the difference in concentration of a substance inside versus outside of the membrane àconcentration gradient.

  • more O_2 & Na^+ outside of the cell membrane

  • more CO_2 and K^+ inside of the cell membrane

• The membrane can maintain a difference in charged ions between inside & outside of the membrane (electrical gradient or membrane potential).

• Thus, substances move down their concentration gradient and towards the oppositely charged area.

• Therefore, ions have electrochemical gradients.

Passive Transport

• No cellular energy (ATP) required.

• Substance moves down its concentration gradient.

• Two (2) types of passive transport

  1. Diffusion: 3 types:

     • Simple diffusion

     • Facilitated diffusion:

       • Carrier-mediated

       • channel-mediated

     • Osmosis

  2. Filtration

     • Usually takes place across capillary walls

Diffusion

• Collisions cause molecules to move down or with their concentration gradient.

• Difference in concentration between two areas.

• O_2 generally diffuses into cells because it is more concentrated outside of them.

• CO_2 typically diffuses out of cells because it is more concentrated inside of them.

• The speed of diffusion is influenced by the size of the molecule and temperature.

• When the molecules are evenly distributed, equilibrium has been reached.

• Molecules will passively diffuse through the membrane if

  • The membrane is lipid soluble, or

  • The molecule is small enough to pass through membrane channels, or

  • The molecule is assisted/Mediated by a carrier or channel protein.

  • Simple Diffusion

    • Where nonpolar, lipid-soluble (hydrophobic) substances diffuse directly through the phospholipid bilayer, e.g., O2, CO2, and fat-soluble vitamins

  • Facilitated Diffusion: Carrier-mediated and channel-mediated(2 types)

    • The diffusion process is used for those substances that cannot cross the lipid bilayer due to their size and/or polarity, e.g., The glucose molecule needs a specialized carrier protein called a transporter (glucose transporter) to facilitate the movement of glucose into the cell.

    • Carrier proteins:

      • Uniport: movement of 1 specific substance across the membrane

      • Symport (cotransport): movement of 2 substances in the same direction across the cellular membrane

      • Antiporter (countertransport): movement of 2 different substances in the opposite directions across the cell membrane

Osmosis

• Net diffusion movement of water (the solvent) through a semipermeable membrane from an area of high water (H_2O) concentration to an area of lower water concentration by:

  • diffusion through the lipid bilayer

  • aquaporins (transmembrane proteins) that function as water channels

• Osmosis only occurs if the membrane is permeable to water but not to certain solutes.

• Osmosis occurs when water concentration is different on the two sides of a membrane.

• Water concentration varies with the number of solute particles because solute particles displace water molecules.

• Osmolarity: Is the measure of the total concentration of solute particles.

• When solutions of different osmolarity are separated by a membrane permeable to all molecules, both the solutes and the water cross the membrane until equilibrium is reached.

• When solutions of different osmolarity are separated by membrane impermeable to the solutes, osmosis occurs until equilibrium is reached.

• Can cause cells to swell or shrink.

• Change in cell volume disrupts cell function, especially in neurons.

• Osmosis occurs when there is an imbalance of solutes outside of a cell versus inside the cell.

• Osmosis involves 2 solutions

  • ECF solution

  • ICF solution

  • There are 3 possible Osmolarity relationships of these 2 solutions: Tonicity.

    1. Isotonic Solution

    2. Hypotonic Solution

    3. Hypertonic Solution

• Tonicity: Is the ability of a solution to alter a cell's water volume

  • Isotonic Solution: Is a Solution with the same non-penetrating solute concentration as that of the cell’s cytosol.

  • Hypertonic Solution: Is a Solution with a higher non-penetrating solute concentration than the cell’s cytosol.

  • Hypotonic Solution: Is a Solution with a lower non-penetrating solute concentration than the cell’s cytosol.

Filtration

• Uses a hydrostatic pressure gradient (water pressure) that pushes the fluid from a higher pressure area to a lower pressure area.

• This is an extremely important process in the body,

• Especially in the circulatory and renal systems.

Active Transport Processes

• Two types of active transport processes

  • Active transport

  • Vesicular transport

• ATP is required to move a substance across a membrane, often with the help of protein carriers and usually against its concentration gradient.

• Both processes require ATP to move solutes across a living plasma membrane because

  • Solute too large for channels

  • Solute not lipid soluble

  • Solute is not able to move down its concentration gradient

  • One of the most common types of active transport involves proteins that serve as “PUMPS.”

Active Transport

• Requires carrier proteins (solute pumps) e.g.,

  • The sodium-potassium Pump: aka Na^+/K^+ ATPase, a very important ion pump.

    • A pump binds specifically and reversibly with the substance being transported.

    • A pump moves the solutes against their concentration gradient.

    • A pump requires energy (ATP)

• There are 2 types of Active Transport:

  • Primary active transport

    • It requires energy directly from the hydrolysis of ATP.

  • Secondary active transport

    • It requires energy indirectly from the ionic gradients created by the primary active transport process.

Primary Active Transport: The sodium-potassium Pump

• Is a very important ion pump, found in the membranes of many types of cells.

• Particularly abundant in nerve cells, which are constantly pumping out sodium ions and pulling in potassium ions to maintain an electrical gradient across their cell membrane.

• An electrical gradient is a difference in electrical charge across space.

• This process is so important for nerve cells that it accounts for the majority of their ATP usage.

• The sodium-potassium pump moves sodium and potassium ions in opposite directions, each against its concentration gradient.

• In a single cycle of the pump, three sodium ions are extruded from and two potassium ions are imported into the cell.

Vesicular Transport

• Does not involve membrane carriers

• It is the transport of large particles, macromolecules, and fluids across the membrane in membranous sacs called vesicles.

• Requires cellular energy à ATP

• 4 major types of Vesicular Transport:

  • Exocytosis

    • The transport of a substance out of the cell; hormone secretion, neurotransmitter release, mucus secretion, and ejection of wastes

  • Endocytosis

    • The transport of substance into the cell; 3 types

      • Phagocytosis

        • The endocytosis of large particles. Immune cells use this against invading pathogens.

      • Pinocytosis

        • Brings into the cell fluid containing dissolved substances.

      • receptor-mediated endocytosis

        • Is endocytosis by a portion of the cell membrane containing receptors specific for a certain substance.

        • Receptor-ligand complexes

  • Transcytosis

    • The transport of a substance into, across, and then out of the cell.

  • Vesicular trafficking

    • The transport of a substance from one area or organelle in the cell to another area or organelle.

The Cytoplasm and Cellular Organelles

• All living cells in multicellular organisms contain an internal cytoplasmic compartment and a nucleus within the cytoplasm.

• Cytosol (ICF)

  • The jelly-like substance within the cell;

  • 55% of cell volume

  • A fluid medium is necessary for the cell’s biochemical reactions.

• Organelle (“little organ”)

  • Is one of several different types of membrane-enclosed bodies in the cell.

  • Most with membranes, but some without

  • They are the Metabolic machinery of the cell

  • Each performs a unique function.

• Cytoplasm

  • The organelles and the cytosol taken together.

• Nucleus

  • Is the cell’s central organelle.

  • Contains the cell’s DNA.

Organelles in the Cytoplasm

• With Membranes (membranous)

  • Mitochondria

  • Peroxisomes

  • Lysosomes

  • Endoplasmic reticulum

  • Golgi apparatus

• Without Membranes (non-membranous)

  • Cytoskeleton

  • Centrioles

  • Ribosomes

• Membranes allow crucial compartmentalization of metabolic activities.

Organelles of the Endomembrane System

• A set of 3 organelles forms this system:

  • Endoplasmic reticulum (ER)

  • Golgi apparatus

  • Vesicles

• These organelles work together to perform various cellular jobs:

  • Producing cellular products

  • Packaging cellular products

  • Exporting certain cellular products.

Endoplasmic Reticulum (ER)

• A system of interconnected channels (tubes) and parallel membranes enclosing cisterns that is continuous with the outer nuclear membrane (or “envelope”) covering the nucleus and composed of the same lipid bilayer material.

• The ER provides passages throughout much of the cell that function in:

  • Transporting materials

  • Synthesizing materials

  • Storing materials.

• The winding structure of the ER results in a large membranous surface area that supports its many functions.

Two varieties of Endoplasmic Reticulum (ER)

1. Rough ER (RER)

   • So-called because its membrane is dotted with embedded granules, organelles called ribosomes, which give it a bumpy microscopic appearance.

   • Its primary job is synthesizing & modifying proteins destined for the cell membrane or for export from the cell.

   • Ribosomes serve as the sites of protein synthesis.

   • Composed of 2 ribosomal RNA subunits that wrap around mRNA to start the process of translation, followed by protein synthesis.

2. Smooth ER (SER)

   • Lacks ribosomes

   • One main function is the synthesis of lipids: phospholipids & steroid hormones

   • Sequesters & regulates the concentration of cellular Ca^{2+}

   • Metabolizes some carbohydrates & performs a detoxification role

   • Free ribosomes synthesize soluble proteins that function in the cytosol or other organelles.

The Golgi Apparatus

• Responsible for sorting, modifying, and shipping off the products that come from the rough ER.

• Consists of 3-20 flattened, curved membranous sacs called cisterns

• Has 2 distinct sides, each with a different physiological role:

  • The Convex (cis face) side faces the ER.

  • The Concave (trans face) side faces the cell membrane.

  • The protein released from the trans face is repackaged into new vesicles.

  • If the product is to be exported (secreted) from the cell, the vesicle migrates to the cell surface and fuses to the plasma membrane and is secreted.

Vesicles

• Three types of vesicles bud off the concave trans face of the Golgi apparatus:

  • Secretory vesicles (granules)

    • From trans face; release exported proteins by exocytosis

  • Vesicles of lipids and transmembrane proteins for the plasma membrane or organelles

  • Lysosomes that remain in the cell

    • The lysosome is an organelle that contains enzymes that break down & digest unneeded cellular components, such as a damaged organelle; pH reaches 5.

    • Autophagy (autophagosome): “self-eating” is the process of a cell digesting its own structures.

    • Important for breaking down foreign material à bacteria & viruses

    • In the case of damaged or unhealthy cells, lysosomes can be triggered to open up & release their digestive enzymes into the cytoplasm of the cell à “self-destruction” called autolysis, process of programmed cell death à “apoptosis.”

The Mitochondrion

• Is a double membrane, bean-shaped organelle that is the “energy transformer” of the cell.

• Its central cavity is known as the matrix.

• Its inner membrane folds are known as cristae.

• The Cristae surface area is used for the chemical reactions of cellular respiration à C6H{12}O6 + 6O2 → 6CO2 + 6H2O + energy (ATP)

• Its Function:

  • Major site of ATP synthesis when oxygen is available

  • “energy transformer” or “energy-conversion factory à the powerhouse of the cell

• Mitochondria can self-replicate.

  • Increases with the need for ATP only inherited from mother

The Peroxisome

• Is a membrane-bound organelle that contains an abundance of enzymes (oxidases & catalases) used for detoxifying harmful substances & lipid metabolism.

• In contrast to the digestive enzymes found in lysosomes, the enzymes within peroxisomes serve to transfer hydrogen atoms from various molecules of oxygen, producing hydrogen peroxide (H2O2).

• This neutralizes dangerous free radicals, which are highly reactive chemicals with unpaired electrons.

• In this way, peroxisomes detoxify harmful or toxic substances, such as alcohol.

• To appreciate the importance of peroxisomes, one must understand the concept of the “reactive oxygen species” (ROS).

Reactive Oxygen Species (ROS)

• Peroxides (O_2^{2-}) and free radicals are highly reactive products of many normal cellular processes, including the mitochondrial reactions that produce ATP.

• Hydroxyl radical OH, superoxide (O_2^-

• Some ROS are important for certain cellular functions:

  • Signaling processes

  • Immune responses

• Free radicals are reactive because they contain free unpaired electrons.

• They can easily oxidize other molecules throughout the cell, causing:

  • Cellular damage and even cell death.

• Peroxisomes oversee reactions that neutralize free radicals.

• They produce large amounts of toxic H2O2 in the process.

• They contain enzymes (catalases) that convert the H2O2 into water & oxygen that are safe to release into the cytoplasm.

• Like miniature sewage plants, they neutralize harmful toxins so that they do not wreak havoc in the cells.

• The liver is the organ primarily responsible for detoxifying the blood before it travels throughout the body.

• Liver cells contain an exceptionally high #s of peroxisomes.

• The defense mechanisms of detoxification within the peroxisomes and certain cellular antioxidants serve to neutralize these ROS.

• Some vitamins and other substances, found primarily in fruits & vegetables, have antioxidant properties.

• Antioxidants work by being oxidized themselves thus, halting the destructive reaction cascades initiated by the free radicals.

• However, sometimes the ROS accumulate beyond the capacity of such defenses.

Oxidative Stress

• Term used to describe damage to cellular components caused by ROS.

• ROS can set off cascades of reactions where they remove electrons from other molecules, which then become oxidized and reactive, and do the same to other molecules.

• ROS can cause permanent damage to:

  • Cellular lipids, proteins, carbohydrates, and nucleic acids.

  • Damaged DNA can lead to genetic mutations and even cancer.

• Many diseases are believed to be triggered or exacerbated by ROS:

  • Alzheimer’s, cardiovascular diseases, and diabetes to name a few.

• Many scientists believe that oxidative stress is a major contributor to the aging process.

The Cytoskeleton

• Elaborate series of fibrous protein rods that run throughout the cytosol, providing structural support for the cell.

• Cytoskeletal components are also critical for:

  • Cell motility

  • Cell reproduction

  • Transportation of substances within the cell

• The cytoskeleton forms a complex thread-like network throughout the cell consisting of three different kinds of protein-based filaments:

  • Microtubules

  • Microfilaments

  • Intermediate filaments

Microtubules

• Thickest of the 3 cytoskeletal elements; dynamic hollow cylindrical tubes; composed of protein subunits called tubulins.

• Maintain cell shape and structure and play a role in the distribution of the organelles within the cell; help resist compression of the cell.

• They make up 2 types of cellular appendages important for motion:

  • Cilia

    • Found many cells of the body and move rhythmically so as to move substances about in the body.

  • Flagellum

    • Larger than a cilium & specialized for cell locomotion à sperm cell.

• A very important function of microtubules is to set the paths (somewhat like railroad tracks) along which the genetic material can be pulled during cell division, so that each new daughter cell receives the appropriate set of chromosomes.

• Two short, identical microtubule structures called centrioles are found near the nucleus of cells.

• A centriole can serve as the cellular origin point for microtubules extending outward as cilia or flagella or can assist with the separation of DNA during cell division. Each is composed of a circle of 9 triplets of microtubules.

• Microtubules grow out from the centrioles by adding more tubulin subunits, like adding additional links to a chain.

• Form mitotic spindle during cell division; unpaired centrioles form basal bodies of cilia and flagella.

Microfilaments

• Thinnest of the cytoskeletal elements, composed primarily of strands of a protein called actin.

• Actin fibers, which are twisted chains of actin filaments, constitute a large component of muscle tissue and, along with the motor protein myosin, are responsible for muscle contraction.

• They form a dense web attached to the cytoplasmic side of the plasma membrane, which is called the terminal web.

• This web gives strength and compression resistance to a cell and is involved in cell motility, changes in cellular shape, endocytosis, and exocytosis.

Intermediate Filaments

• A filament intermediate in thickness between the microtubules and microfilaments.

• Tough, insoluble, long fibrous subunits of the protein keratin that compose ropelike threads anchor organelles that help the cell.

• Resist pulling forces; attach to desmosomes, work with microtubules to help the cell maintain its shape and structure, and resist tension, the forces that would pull apart the cell, e.g., neurofilaments in nerve cells; keratin filaments in epithelial cells in the skin.

The Nucleus

• Largest organelle and usually the only organelle visible with the light microscope; considered the control center of the cell because it stores all of the genetic instructions (DNA) that determines the entire structure and function of the cell.

• Responds to signals and dictates the kinds and amounts of proteins to be synthesized.

• Some cells in the body, such as skeletal muscle cells, contain more than one nucleus, known as multinucleated, most are à uninucleate; the mature RBC has ejected its nucleus making more room for hemoglobin that carries oxygen. à anucleate.

• Surrounded by a membrane called the nuclear envelope (NE), which consists of 2 adjacent lipid bilayers with a thin fluid space in between them.

• Spanning the 2 bilayers are nuclear pores; these pores are tiny passageways for the passage of proteins, RNA, and solutes between the nucleus and the cytoplasm.

• Proteins called pore complexes lining the nuclear pores regulate the passage of materials into & out of the nucleus.

• Inside the NE is a gel-like nucleoplasm with solutes that include the blocking blocks of nucleic acids. In the nucleoplasm is a dark-staining mass called the nucleolus: a region of the nucleus that is responsible for manufacturing the rRNA necessary for the construction of ribosomes.

• Once synthesized, the newly made ribosomal subunits exit the cell’s nucleus through the nuclear pores.

DNA

• The genetic instructions that are used to build and maintain an organism are arranged in an orderly manner in strands of DNA.

• Within the nucleus are threads of chromatin, which is composed of DNA (30%), associated proteins (60%) and RNA (10%).

• Along the chromatin threads, the DNA is wrapped around a set of histone proteins (DNA-histone complex) that are arranged in fundamental units called nucleosomes.

• When a cell is in the process of dividing, the chromatin condenses into bar-like bodies called chromosomes.

• A chromosome is composed of DNA and proteins and is the condensed form of chromatin.

• It is estimated that humans have almost 22,000 genes distributed on 46 chromosomes.

DNA Replication

• For an organism to grow, develop, and maintain its health, cells must reproduce themselves by dividing to produce 2 new daughter cells, each with the full complement of DNA as found in the original cell.

• Billions of new cells are produced in an adult human every day.

• Only a few cell types in the body do not divide, such as nerve cells, skeletal muscle cells, and cardiac muscle cells.

• The division time of different cell types varies; epithelial skin and GI lining cells divide very frequently.

• A DNA molecule is made of 2 strands that “complement” each other, creating a double-stranded molecule that looks much like a long, twisted ladder à the DNA double helix.

• Each strand is composed of alternating sugar & phosphate groups; the 2 strands are not identical but are complementary.

• These 2 backbone strands are bonded to each other across pairs of protruding bases, each hydrogen-bonded pair forming one “rung” of the ladder.

• The 4 DNA bases are adenine, thymine, cytosine, and guanine.

• Because of the bases’ shape and charge, the 2 bases that compose a “pair” always bong together:

  • Adenine always binds with Thymine (A-T).

  • Cytosine always binds with Guanine (C-G).

• The particular sequence of bases along the DNA molecule determines the genetic code.

• Therefore, if the 2 complementary strands of DNA were pulled apart, you could infer the order of the bases in one strand from the bases in the other, Complementary strand.
  *Example, if one strand has a region with the sequence AGTGCCT, then the sequence of the complementary strand would be TCACGGA.

Stages of DNA Replication

1. Initiation

   • The 2 complementary strands are separated, much like a zipper; special enzymes, including helicase, untwist and separate the 2 strands of DNA.

2. Elongation

   • Each strand becomes a template along which a new complementary strand is built; DNA polymerase brings in the correct bases to complement the template strand, synthesizing a new strand base by base; is an enzyme that adds free nucleotides to the end of a chain of DNA, making a new double strand; this growing strand continues to be built until it has fully complemented the template strand.

3. Termination

   • Once the 2 original strands are bound to their own, finished, complementary strands, DNA replication is stopped and the 2 “new identical” DNA molecules are complete. Each new DNA molecule contains 1 strand from the original molecule and 1 newly synthesized strand. The term for this mode of replication is “semiconservative” because half of the original DNA molecule is conserved in each new DNA molecule.

• This process continues until the cell’s entire genome is replicated; genome is the entire complement of an organism’s DNA.

• It is very important that DNA replication is precisely performed; do not want mistakes that could render a gene dysfunctional or useless à disease.

• A DNA proofreading process enlists the help of special enzymes that can scan the newly synthesized molecule for mistakes and corrects them. Once the process of DNA replication is complete, the cell is ready to divide.

Protein Synthesis

• Most structural components of the cell are made up, at least in part, by proteins, and virtually all the functions that a cell carries out are completed with the help of proteins.

• One of the most important classes of proteins is enzymes, which help speed up necessary biochemical reactions that take place inside the cell; no enzymes, no life!

• Proteome is the cell’s full complement of proteins; protein synthesis begins with genes.

• A gene is a functional segment of DNA that provides the genetic information necessary to build a protein; each particular gene provides the code necessary to construct a particular protein.

• Gene expression, is the transformation of the information coded in a gene to a final gene product; it ultimately dictates the structure and function of a cell by determining which proteins are made.

• The interpretation of genes works in the following way: the sequence of bases in a gene (that is, its sequence of A, T, C, G nucleotides) translates to an amino acid sequence.

• A triplet is a section of 3 DNA bases in a row that codes for a specific amino acid; Example, the DNA triplet CAC (cytosine, adenine, and cytosine) specifics the amino acid valine.

• Therefore, a gene, which is composed of multiple triplets in a unique sequence, provides the code to build an entire protein, with multiple amino acids in the proper sequence.

• The mechanism by which cells turn the DNA code into a protein product is a 2-step process, with an RNA molecule as the intermediate:

  • Transcription: DNA à mRNA

  • Translation: mRNA à Protein

• DNA is housed within the nucleus; protein synthesis takes place in the cytoplasm, so there must be some sort of “intermediate messenger” that leaves the nucleus and manages protein synthesis in the cytoplasm. It is messenger RNA (mRNA), a single-stranded nucleic acid that carries a copy of the genetic code for a single gene out of the nucleus and into the cytoplasm where it is used to produce proteins.

• There are 3 different types of RNA, all formed on DNA in the nucleus and each having different functions in the cell (mRNA, rRNA, and tRNA).

• The structure of RNA is similar to DNA except:

  • RNA is single-stranded and contains no complementary strand.

  • The ribose sugar in RNA contains an additional oxygen atom.

  • RNA instead of using the nitrogenous base thymine, uses the base uracil, which means that in RNA, the base adenine will always pair with the base uracil during the protein synthesis process.

Transcription: DNA → mRNA

• Gene expression begins with the process called transcription: the synthesis of a strand of mRNA that is complementary to the gene of interest.

• Transcription begins when a small portion of DNA unwinds and splits apart; the triplets within the gene on this section of the DNA molecule are used as the template to transcribe the complementary strand of RNA.

• A codon is a 3-base sequence of mRNA, so-called because the 3-base sequence directly encodes amino acids. Like DNA replication, there are 3 stages to transcription:

  • Initiation

  • Elongation

  • Termination

Stages of Transcription

1. Initiation

   • A region at the beginning of the gene called a promoter, a particular sequence of nucleotides, triggers the start of transcription.

2. Elongation

   • Transcription starts when RNA polymerase unwinds the DNA segment. RNA polymerase is an enzyme that adds new nucleotides to a growing strand of RNA; this process builds a strand of mRNA.

   • The polymerase then aligns the correct nucleic acid (A, C, G, or U) with its complementary base on the coding strand of DNA.

3. Termination

   • When the polymerase has reached the end of the gene, one of 3 specific triplets (UAA, UAG, or UGA) codes a “stop” signal, which triggers the enzymes to terminate transcription and release the mRNA transcript.

• Before the mRNA molecule leaves the nucleus and proceeds to protein synthesis in the cytoplasm, it is modified in a number of ways; for this reason, it is often called a pre-mRNA at this stage.

• Your DNA, and thus complementary mRNA, contains long regions called non-coding regions that do not code for amino acids.

• Their function is still a mystery, but the process called splicing removes these non-coding regions from the pre-mRNA transcript.

• A spliceosome, a structure composed of various proteins and other molecules, attaches to the pre-mRNA and “splices” or cuts out the non-coding regions.

• The removed segment of the transcript is called an intron ; some introns removed from mRNA are not always non-coding. The remaining exons are pasted together.

• An exon is a segment of RNA that remains after splicing and contains the protein-coding sequence.